SMTL ID : 4kmt.1

Crystal structure of human germline antibody 5-51/O12

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-mer

Ligands

3 x NHE: 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID(Non-covalent)

NHE.1: 7 residues within 4Å: Chain A: V.115, F.116, I.117, K.207 Chain B: T.141 Ligands: NHE.7, GOL.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.117 Water bridges: A:S.208 NHE.6: 3 residues within 4Å: Chain B: S.162, N.203, D.214 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.203, B:D.214 Water bridges: B:S.162 NHE.7: 12 residues within 4Å: Chain A: F.116, I.117, F.118, P.119, F.209, C.214 Chain B: A.131, P.132, S.133, A.142, A.143 Ligands: NHE.1 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:P.119, A:F.209 Hydrogen bonds: B:S.133, B:A.143, B:A.143

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 6 residues within 4Å: Chain A: L.96, T.97, F.98 Chain B: L.45, E.46, W.47 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:W.47, A:L.96, A:F.98 Water bridges: A:T.97 SO4.8: 3 residues within 4Å: Chain A: T.94 Chain B: R.59 Ligands: GOL.10 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:R.59 Hydrogen bonds: A:T.94, A:T.94 SO4.9: 3 residues within 4Å: Chain B: Y.27, S.28, Y.32 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.28, B:Y.32 Water bridges: B:Y.32

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 12 residues within 4Å: Chain A: Q.160, E.161, S.162, S.176, S.177, T.178 Chain B: F.172, P.173, V.175, S.183, L.184, S.185 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:F.172, B:S.183, B:S.185, A:Q.160, A:S.162, A:T.178 GOL.4: 6 residues within 4Å: Chain A: S.121, D.122, E.123 Chain B: P.129, K.215, K.220 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.122, A:D.122, A:E.123, A:E.123, A:E.123, B:K.215 GOL.5: 3 residues within 4Å: Chain A: S.30, Y.32, Y.92 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.30, A:Y.32 GOL.10: 4 residues within 4Å: Chain B: W.33, R.59, Y.99 Ligands: SO4.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.59, B:R.59, B:Y.99 GOL.11: 1 residues within 4Å: Chain B: K.19 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.19 Water bridges: B:K.19, B:K.19 GOL.12: 2 residues within 4Å: Chain B: G.140, S.192 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.140, B:G.140, B:S.192 GOL.13: 3 residues within 4Å: Chain B: G.140, T.141 Ligands: NHE.1 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.141 Water bridges: B:T.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Teplyakov, A. et al., Antibody modeling assessment II. Structures and models. Proteins (2014)

Release Date

2014-03-26

Peptides

light chain O12/KAPPA: A
heavy chain 5-51/CNTO888/IGG1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

light chain O12/KAPPA

heavy chain 5-51/CNTO888/IGG1

Related Entries With Identical Sequence